I agree that the dynamic feel of a guitarist's playing will be altered when tracking through an amp sim...if the amp sim isn't set to respond the way the player is used to. If you plan on reamping through a real amp later, but you don't take the time to tweak an amp sim with the guitar player, then you're immediately going to be headed for trouble. Firing up the POD and just saying "Here, track through this BRVTAL metal patch I love...ready, set, GO!" does not sound like a professional approach at all. And honestly, I think a guitar player would be kind of stupid if he was sitting down to record a song, and didn't speak up if the amp sim tone didn't feel normal to play though. If we're talking about capturing the best performances of everyone in the band, then to me it's of the utmost importance to make sure that the guitarist feels comfortable with the tone he's hearing. Yeah, there are inherent differences between the sound/feel of an amp and the sound/feel of an amp sim, but I don't think that the difference is irreconcilable to the point that guitar players cannot perform comfortably through an amp sim and record DI tracks that translate well to a real amp. As a guitar player myself, I would never want to record guitars and feel like I was adjusting my playing to accommodate a peculiar amp tone! The amp sim should be set to accommodate the guitarist, not the other way around! I can tell when I'm playing comfortably and playing the way I am used to, as any solid guitarist should, and I have never found it impossible to dial in an amp sim to work for me.
Once you've got that nailed, then the only possible loss of quality during reamping is the fidelity of the DI tracks themselves...and if you have a decent converter, a good DI box, and a clean sounding preamp, and a good reamp box, then I don't think there should be any issues whatsoever!